Yong Li

Root-knot nematodes ( Meloidogyne spp.) damage peach trees, and one of the most effective ways instead of the most fundamental way as there are other management strategies. We compared root transcriptomes of resistant ‘Nemaguard’ and susceptible ‘Bailey’ after inoculation with Meloidogyne incognita , the southern root-knot nematode. Roots were sampled at 0, 3, 6, 9, 12, and 24 h after inoculation. Both genotypes showed the strongest transcriptional response at 24 h. Differential expression and Gene Ontology (GO) analyses identified 14 candidate genes for defense and signaling. These included 13 resistance (R) genes and one signaling-related gene. We tested the expression of 14 candidates by qRT-PCR. Their expression patterns agreed with the RNA-seq results. The candidates can now be tested for their roles in peach resistance to M. incognita .

Powdery mildew is one of the major diseases of peach. To clarify the relationships between peach powdery mildew resistance and leaf structure and defensive enzyme activities, this study used the resistant genotype ‘Zhou Xing Shan Tao’ (Prunus davidiana) and the susceptible genotype ‘Shache Lürou No.3’ (Prunus ferganensis) as a control. Resistance was evaluated through artificial inoculation with powdery mildew conidia (Podosphaera tridactyla). Key indicators including leaf wax content, stomatal characteristics, leaf transverse structure, and the activities of three defense enzymes were assessed and the relationship between these traits and resistance was analyzed. The results showed that ‘Zhou Xing Shan Tao’ exhibited stronger resistance to powdery mildew than ‘Shache Lürou No.3’. ‘Zhou Xing Shan Tao’ leaves exhibited a significantly higher (p < 0.01) wax content and a significantly lower stomatal density relative to ‘Shache Lürou No.3’. However, the size of individual stomata (long diameter, short diameter, circumference, area) did not differ significantly between the two genotypes. Microstructurally, ‘Zhou Xing Shan Tao’ leaves had significantly greater fenestrated tissue, lower epidermis, palisade cell layers, and overall leaf thickness. Its leaf tissue structure was also significantly more compact, with a higher compactness-to-openness ratio, and significantly less cellular laxity than ‘Shache Lürou No.3’. Following inoculation with powdery mildew, ‘Zhou Xing Shan Tao’ leaves accumulated hydrogen peroxide (H₂O₂) and malondialdehyde (MDA) more rapidly and to a greater extent. The activities of the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) defense enzymes also increased faster and were significantly higher than in ‘Shache Lürou No.3’. In conclusion, leaf structural traits such as wax content and stomatal density combined with pathogenicity assessments serve as effective phenotypic indicators for evaluating powdery mildew resistance in Prunus species.

Bud mutation is an important solution in fruit breeding, but the mechanism of bud mutation remains largely unknown. Here, we present the phenotypic, genomic, and transcriptomic analyses of a peach hairless bud mutation. Phenotypic analyses found an increase in the soluble solid content (SSC), fructose, and glucose, as well as a decrease in fruit weight, sucrose, and sorbitol in hairless bud mutation. Genomic analyses showed a higher number of SNPs, indels, SVs, and TEs in the hairless bud mutation than the wild type. Moreover, most of the variations were heterozygous. An LTR transpose element in the third exon of PpMYB25 was identified in the hairless mutation, but was absent in the wild type, underlying the hairless phenotype. A total of 660 differentially expressed genes were identified in mutation, including 254 were upregulated and 406 were downregulated. The functional annotation of differentially expressed genes revealed two sucrose synthase gene PpSUS3 and PpSUS4, as well as two nitrate transporter gene PpNRT2.5 and PpNRT1, implying the candidates underlying the increase in the SSC and decrease in the fruit weight in mutation. Our results elucidated the complicated impacts of bud mutation on the genome and transcriptome provide new insights into, providing new insights into the molecular mechanism of somatic mutation in plants.

The spatiotemporal transcriptome dataset reported here provides the peach flower bud’s gene expression atlas at spatiotemporal resolution level using the 10x Genomics Visium platform. This dataset can be used to define transcript accumulation for any interesting genes across several flower bud cells. It was generated using three peach flower bud samples during the activity–dormancy period, providing valuable insight into gene expression profiling and developmental stages under different environmental contexts or conditions. Importantly, we found that different cell types are related to specific regulatory programs, including signal transduction, environment and stress responses, and flower development. Our research provides insight into the transcriptomic landscape of the key cell types for flower buds and opens new avenues to study cell-type specification, function, and differentiation in Rosaceae fruit trees. A series of pivotal genes (e.g. AMS, MS188, MS1) for flower bud development were identified. These results provide a valuable reference for the activity–dormancy transition in perennial deciduous fruit trees.

Modern breeding technologies and the development of quantitative trait locus (QTL) mapping have brought about a new era in peach breeding. This study examines the complex genetic structure that underlies the morphology of peach fruits, paying special attention to the interaction between genome editing, genomic selection, and marker-assisted selection. Breeders now have access to precise tools that enhance crop resilience, productivity, and quality, facilitated by QTL mapping, which has significantly advanced our understanding of the genetic determinants underlying essential traits such as fruit shape, size, and firmness. New technologies like CRISPR/Cas9 and genomic selection enable the development of cultivars that can withstand climate change and satisfy consumer demands with unprecedented precision in trait modification. Genotype–environment interactions remain a critical challenge for modern breeding efforts, which can be addressed through high-throughput phenotyping and multi-environment trials. This work shows how combining genome-wide association studies and machine learning can improve the synthesis of multi-omics data and result in faster breeding cycles while preserving genetic diversity. This study outlines a roadmap that prioritizes the development of superior cultivars utilizing cutting-edge methods and technologies in order to address evolving agricultural and environmental challenges.

Peach (Prunus persica) landrace has typical regional characteristics, strong environmental adaptability, and contains many valuable genes that provide the foundation for breeding excellent varieties. Therefore, it is necessary to assemble the genomes of specific landraces to facilitate the localization and utilization of these genes. Here, we de novo assembled a high-quality genome from an ancient blood-fleshed Chinese landrace Tianjin ShuiMi (TJSM) that originated from the China North Plain. The assembled genome size was 243.5 Mb with a contig N50 of 23.7 Mb and a scaffold N50 of 28.6 Mb. Compared with the reported peach genomes, our assembled TJSM genome had the largest number of specific structural variants (SVs) and long terminal repeat-retrotransposons (LTR-RTs). Among the LTR-RTs with the potential to regulate their host genes, we identified a 6688 bp LTR-RT (named it blood TE) in the promoter of NAC transcription factor-encoding PpBL, a gene regulating peach blood-flesh formation. The blood TE was not only co-separated with the blood-flesh phenotype but also associated with fruit maturity date advancement and different intensities of blood-flesh color formation. Our findings provide new insights into the mechanism underlying the development of the blood-flesh color and determination of fruit maturity date and highlight the potential of the TJSM genome to mine more variations related to agronomic traits in peach fruit.

Single fruit weight is an important goal of crop production and horticultural species domestication, but its genetic mechanism is still unclear. In this study, the fruits of different peach fruit types in their first rapid development period were used as materials. First, the differentially expressed genes were analyzed by RNA-seq data. Secondly, weighted gene co-expression network analysis (WGCNA) was used to calculate the correlation between genes and modules, the genes with different expression patterns were divided into 17 modules, the modules were correlated with the phenotype of single fruit, and a highly correlated blue module was obtained. Then, the possible differentially expressed genes and signal pathways among different fruit types were compared by gene set enrichment analysis (GSEA) and 43 significant pathways were obtained. Finally, 54 genes found to be repeatedly expressed in 3 of the methods were screened, and 11 genes involved in plant hormone signal transduction were selected for subsequent analysis according to their functional annotations. Combined with the changing trend of phenotype, three genes (Prupe.7G234800, Prupe.8G079200 and Prupe.8G082100) were obtained as candidate genes for single fruit weight traits. All three genes are involved in auxin signal transduction, with auxin playing an important role in plant growth and development. This discovery provides a new perspective for revealing the genetic law of single fruit weight in peach.

As a foundation to understand the molecular mechanisms of peach evolution and high-altitude adaptation, we performed de novo genome assembling of four wild relatives of P. persica, P. mira, P. kansuensis, P. davidiana and P. ferganensis . Through comparative genomic analysis, abundant genetic variations were identified in four wild species when compared to P. persica . Among them, a deletion, located at the promoter of Prupe.2G053600 in P. kansuensis , was validated to regulate the resistance to nematode. Next, a pan-genome was constructed which comprised 15,216 core gene families among four wild peaches and P. perisca . We identified the expanded and contracted gene families in different species and investigated their roles during peach evolution. Our results indicated that P. mira was the primitive ancestor of cultivated peach, and peach evolution was non-linear and a cross event might have occurred between P. mira and P. dulcis during the process. Combined with the selective sweeps identified using accessions of P. mira originating from different altitude regions, we proposed that nitrogen recovery was essential for high-altitude adaptation of P. mira through increasing its resistance to low temperature. The pan-genome constructed in our study provides a valuable resource for developing elite cultivars, studying the peach evolution, and characterizing the high-altitude adaptation in perennial crops.